Search Results for "source code computer" - Page 7

...Please, send email to thilo.figge<at>hki-jena.de to request a copy of the source code.

Phage_Finder is a heuristic computer program written in PERL that uses BLASTP data, HMM results, and tRNA/tmRNA information to find prophage regions in complete bacterial genome sequences.

MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/

Arena is a computer simulation in which programs compete for CPU time and access to main memory. Processes such as the dynamics of punctuated equilibrium, host-parasite co-evolution and density dependent natural selection are amenable to investigation.

We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.

Displays mummer/nucmer mappings and prints PNG to stdout via the "show-coords -lcdTH" output. The output file is <coords-output>.png. Command line options allow for different features when producing the image. Within the code there are comment blocks which give examples of how to further customize it i.e. grouping based on name similarity, color, etc. This program is aimed at providing full customization within the limits of the Bio-Graphics module. Current version supported is Bio-Graphics-2.25

This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the...

A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions

This is a Python program based on the NegEx algorithm that detects the polarity of the clinical evidence in clinical random trials. If you use this code please cite this paper: P. Davis-Desmond and Diego Mollá. Detection of Evidence in Clinical Research Papers (2012). Australasian Workshop On Health Informatics and Knowledge Management (HIKM 2012), Melbourne, Australia. http://www.ics.mq.edu.au/~diego/publications/hikm12.pdf

Web application to make user-friendly requests on large XML database. Tools to XML-ize large bodies of semi-formal texts (like floras). Computer-assisted specimen identification. Uses natural language processing, 2D/3D images analysis and generation.

Developed at Medical Research Council UK to meet a common clinical trial need to track various types of clinical data. Users log dates of completed tasks against participant ID. Simple, useable, reduces lost data! Makes graphical progress reports.

Biologic Institute's Stylus simulation software suite. (See the SVN repository for source code.)

Give names to the colors your eyes see, watch the computer learn and suggest names for new randomic colors. It gives the RGB components of each colors and list the memory so on, saving it into a text file with your name.

Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.

ByoDyn (http://cbbl.imim.es/ByoDyn) is a software tool for the study of biochemical networks within the framework of systems biology. SBML compatible, ByoDyn is a group effort of the Computational Biochemistry and Biophysics Lab.

The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.

The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.

""" E-Cell's source code repository has moved to GitHub! https://github.com/ecell The development of E-Cell now continues on GitHub. The Subversion repository was abandoned. """ E-Cell System is an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components driven by multiple algorithms with different timescales to coexist in a model.

Perl code scafflod for the automatic execution of main Next Generation Sequencing data processing and analysis.

Common code developed by researchers in the Edwards Bioinformatics Group at SDSU. This code is free for everyone to use. It is our base code that we provide on an as-is basis. Please let us know if you use the code or have questions/comments

Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.

MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.

SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.

IBIS - Interactive Biodiversity Informatics Software - is software to identify species or other taxa. Intended users range from school children or citizen scientists to ecologists or taxonomists. The identification keys can be embedded in CMS or Wiki

The Blue Obelisk is a group of scientists driven by a belief in Open Source, Open Standards and Open Data, expressed in code, data, algorithms, specifications, tutorials, demonstrations, articles and anything that helps get the message across.